General information for g2994.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Fibroblast growth factor receptor homolog 1.
Parent gene
- The parent gene g2994 is located on chr_3: 21881637..21883664 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g2994 | g2994.t1 | isoform | g2994.t1 | 21875860 | 21881637 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon1 | 21875860 | 21875962 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS1 | 21875860 | 21875962 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon2 | 21878614 | 21879051 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS2 | 21878614 | 21879051 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon3 | 21879526 | 21879704 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS3 | 21879526 | 21879704 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon4 | 21879897 | 21880274 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS4 | 21879897 | 21880274 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon5 | 21880330 | 21880921 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS5 | 21880330 | 21880921 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon6 | 21880976 | 21881105 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS6 | 21880976 | 21881105 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon7 | 21881166 | 21881209 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS7 | 21881166 | 21881209 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon8 | 21881272 | 21881368 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS8 | 21881272 | 21881368 |
| chr_3 | g2994 | g2994.t1 | exon | g2994.t1.exon9 | 21881433 | 21881637 |
| chr_3 | g2994 | g2994.t1 | cds | g2994.t1.CDS9 | 21881433 | 21881637 |
| chr_3 | g2994 | g2994.t1 | TSS | g2994.t1 | NA | NA |
| chr_3 | g2994 | g2994.t1 | TTS | g2994.t1 | NA | NA |
Sequences
>g2994.t1 Gene=g2994 Length=2166
ATGTGCAATAAAAGAATTTTTAAAATATTTTTACTTCTCACTGTCGTTGCATTTCAAGTG
CATTGCAAACACACTGTTGGACTTCGTCGTAACAGAAATTCGGGAAAATATCATTCTGGT
GATTTAGATTCATCAATAATTCGCGATACATCTGACAATGGTGTTGATGATGATCAAATC
GAGACTGAAAGAACATTCACAACGACAGTGACAGCAACAATAAGTACAACAATAAATACA
ACTCAAGAAGGATATGCACCTTATTTTACAAATATGAATGCATTAAACAAAATTAATTTA
AAACCATCAGGAAATATGGTTAAACTCAAATGTCCGGCAAAAGGTGATCCGGAACCAACT
TGGGAATGGACAAAGAATGGAAAACCTATTGAAAGAAAATTAGGAGAGGCAAAAGCGCAA
AACAAGAAGCAAACAGTAATCACACTTGAAGATTTGATTCCAGCTGATAGTGGTACATAT
AATTGTAAAGTATGCAATATTCATGGTTGCATTAATTTTACATCAAAACTTGAAGTTGAA
GAGAGAGTAAATCACAAACCAATTTTTAAAGTACCTCCAAAGAACATTACAGAAATTATT
GGAGCAAATGTGACATTTTTCGTAGAAATTTATTCGGATTATCATCGTTCAATTCAATGG
CTAAAATCTGATTGTAAATATGATGAAAATATTACAACGTGTCATGCAGTGAAGGTTCAG
CGAGACGAAGAAGAGTCTGAAGTGCTACATTTGGAAAATATCACATTTGCTGATGAGGGA
TGGTACACATGTGTAGCTGCAAATACGTTAGGCGCAACGTATGCAAGCGCATATTTACAC
GTTGTTGAGATGCTTCCTTCAGACGGTGACTCGACAAGTATCCGACCCGTGCCGATTAAC
GATTGGTATGGAATTCTCGTAATGTGTCTCATGGTCTCGTTTATGTTCGCTCTTATTATC
ATCATTTTTGTTTGGAAAAAATATACAAAAACTAAAAAGCTGCAACGTCAAATGGAGCGT
GTAAATCAATGGACAAAGAAAGTCATTGTTGTACAACCGTGCATTGATAACGGAAATTCT
GGATTATCTGATTCACTTCAAATGCCAATTGTTAGAATTGAAAAACATCGTTCAACAATG
GCTAGTAATGATCCGAATATGATATCAGAATACGAGTTTCCTATTGATTTGAATTGGGAA
TTTCCACGTAGTCAACTTGAGTTGGGCAAGAATTTGGGAGAAGGTGCATTCGGAAAAGTC
GTAATGGCAAACGCTCACGGCTTAACAAATCCCGGACAATCGATAGTTGTTGCTGTCAAA
ATGTTAAAAGAAGGCCATACGGATGAAGATGTAAAAGACCTTGTATGTGAAATGGAAGTT
ATGAAGATGATTGGAAGACACATAAACATCATTAATTTACTTGGATGCTGCTCACAAGAT
GGTCCACTTTATGTCATAGTAGAATTTGCACCTCATGGAAATTTAAGAGATTTTCTAAGA
AAGCATCGACCAACTGCATATACAGATGTACCAAATGAAAAAGAGAAACAAGCATTGACG
CAAAAAGATCTTGTTTCATTTGCATATCAAATTGCAAGAGGAATGGAATATTTGGCGAGT
CGAAAATGTATTCATAGAGATCTTGCAGCTCGCAATGTTCTTGTTAGTGATGACTTCATT
ATGAAAATTGCTGATTTTGGTCTTGCTCGAGATATTCATTCACAAGATTATTATAGAAAA
ACGACTGATGGAAGATTACCAGTTAAATGGATGAGTCCTGAATCACTTTTTGATAAAGTC
TATGATACTCAAAGTGATGTTTGGTCATATGGCATATTACTATGGGAAATTATGACACTT
GGTGGAACACCATATCCAAGTGTGCCGAGTGTCAAAAATCTTTTTGAATTGCTAAAGAAG
GGTGAACGAATGGATAAACCTGCATTGTGTTCAGTTGATATATATTTATTGATGCGAGAA
TGCTGGCATTGGAATCCAAATGAACGTCCAAATTTTTCTGAAATTGTGGAAGATTTAGAT
AAAATTTTAAGCATCACAGCAAATGAAGAATACTTAGATTTAGGTCTACCTCAACTAGAT
ACACCTCCAAGTTCTAGTGATGAAGAATCCGATGGTGAAGAAGAAAAATTCCCTTATTTA
CTATAA
>g2994.t1 Gene=g2994 Length=721
MCNKRIFKIFLLLTVVAFQVHCKHTVGLRRNRNSGKYHSGDLDSSIIRDTSDNGVDDDQI
ETERTFTTTVTATISTTINTTQEGYAPYFTNMNALNKINLKPSGNMVKLKCPAKGDPEPT
WEWTKNGKPIERKLGEAKAQNKKQTVITLEDLIPADSGTYNCKVCNIHGCINFTSKLEVE
ERVNHKPIFKVPPKNITEIIGANVTFFVEIYSDYHRSIQWLKSDCKYDENITTCHAVKVQ
RDEEESEVLHLENITFADEGWYTCVAANTLGATYASAYLHVVEMLPSDGDSTSIRPVPIN
DWYGILVMCLMVSFMFALIIIIFVWKKYTKTKKLQRQMERVNQWTKKVIVVQPCIDNGNS
GLSDSLQMPIVRIEKHRSTMASNDPNMISEYEFPIDLNWEFPRSQLELGKNLGEGAFGKV
VMANAHGLTNPGQSIVVAVKMLKEGHTDEDVKDLVCEMEVMKMIGRHINIINLLGCCSQD
GPLYVIVEFAPHGNLRDFLRKHRPTAYTDVPNEKEKQALTQKDLVSFAYQIARGMEYLAS
RKCIHRDLAARNVLVSDDFIMKIADFGLARDIHSQDYYRKTTDGRLPVKWMSPESLFDKV
YDTQSDVWSYGILLWEIMTLGGTPYPSVPSVKNLFELLKKGERMDKPALCSVDIYLLMRE
CWHWNPNERPNFSEIVEDLDKILSITANEEYLDLGLPQLDTPPSSSDEESDGEEEKFPYL
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g2994.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 81 | 183 | 1.9E-15 |
| 16 | g2994.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 184 | 285 | 2.8E-17 |
| 18 | g2994.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 366 | 489 | 4.1E-41 |
| 19 | g2994.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 490 | 684 | 4.5E-63 |
| 37 | g2994.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 696 | 721 | - |
| 4 | g2994.t1 | PANTHER | PTHR24416:SF130 | FIBROBLAST GROWTH FACTOR RECEPTOR 2 | 78 | 711 | 1.1E-188 |
| 5 | g2994.t1 | PANTHER | PTHR24416 | TYROSINE-PROTEIN KINASE RECEPTOR | 78 | 711 | 1.1E-188 |
| 27 | g2994.t1 | PIRSF | PIRSF000628 | FGFR | 2 | 717 | 1.2E-257 |
| 7 | g2994.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 487 | 500 | 9.8E-36 |
| 6 | g2994.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 537 | 555 | 9.8E-36 |
| 10 | g2994.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 586 | 596 | 9.8E-36 |
| 9 | g2994.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 605 | 627 | 9.8E-36 |
| 8 | g2994.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 650 | 672 | 9.8E-36 |
| 2 | g2994.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 103 | 179 | 9.6E-11 |
| 3 | g2994.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 188 | 281 | 3.7E-11 |
| 1 | g2994.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 406 | 679 | 1.7E-101 |
| 22 | g2994.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 23 | g2994.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 8 | - |
| 24 | g2994.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 9 | 18 | - |
| 26 | g2994.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 22 | - |
| 21 | g2994.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 301 | - |
| 25 | g2994.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 302 | 325 | - |
| 20 | g2994.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 326 | 721 | - |
| 36 | g2994.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 412 | 440 | - |
| 35 | g2994.t1 | ProSitePatterns | PS00109 | Tyrosine protein kinases specific active-site signature. | 543 | 555 | - |
| 39 | g2994.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 87 | 184 | 12.005 |
| 38 | g2994.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 187 | 280 | 7.449 |
| 40 | g2994.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 406 | 683 | 43.891 |
| 30 | g2994.t1 | SMART | SM00409 | IG_3c | 96 | 180 | 1.0E-6 |
| 34 | g2994.t1 | SMART | SM00408 | igc2_5 | 102 | 169 | 4.8E-12 |
| 31 | g2994.t1 | SMART | SM00409 | IG_3c | 193 | 282 | 4.7E-7 |
| 33 | g2994.t1 | SMART | SM00408 | igc2_5 | 199 | 271 | 0.051 |
| 32 | g2994.t1 | SMART | SM00219 | tyrkin_6 | 406 | 679 | 1.4E-147 |
| 12 | g2994.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 86 | 180 | 3.55E-14 |
| 11 | g2994.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 182 | 282 | 3.97E-16 |
| 13 | g2994.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 378 | 679 | 3.37E-84 |
| 15 | g2994.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 14 | g2994.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 22 | - |
| 29 | g2994.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 260 | 282 | - |
| 28 | g2994.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 302 | 324 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0006468 | protein phosphorylation | BP |
| GO:0005007 | fibroblast growth factor-activated receptor activity | MF |
| GO:0004713 | protein tyrosine kinase activity | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0008543 | fibroblast growth factor receptor signaling pathway | BP |
| GO:0008284 | positive regulation of cell population proliferation | BP |
KEGG
Orthology
- This transcript has been annotated with K05093 (fibroblast growth factor receptor 2)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
